Update OWL file - #195
Conversation
Qodo reviews are paused for this user.Troubleshooting steps vary by plan Learn more → On a Teams plan? Using GitHub Enterprise Server, GitLab Self-Managed, or Bitbucket Data Center? |
📝 WalkthroughWalkthroughTwo new OWL classes, PRIDE:0001011 (broad-scale environmental context) and PRIDE:0001012 (local environmental context), are added to pride_cv.owl, each with subclass relationships, MIXS-based definitions, and standard oboInOwl annotation metadata. ChangesOntology class additions
Estimated code review effort: 1 (Trivial) | ~5 minutes Possibly related PRs
Suggested labels: 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 inconclusive)
✅ Passed checks (4 passed)
✨ Finishing Touches🧪 Generate unit tests (beta)
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 2
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@pride_cv.owl`:
- Around line 19994-20010: Add the missing MIXS field-name synonym annotations
for the PRIDE_0001011 and PRIDE_0001012 class entries so they match the
neighboring MIXS-derived terms. Update each owl:Class block to include the
standard hasExactSynonym and GSCMIXS pair for env_broad_scale and
env_local_scale, keeping the annotations consistent with the existing ontology
pattern and locating the changes by the PRIDE_0001011 and PRIDE_0001012 symbols.
- Around line 20013-20029: Add the missing MIXS synonym/xref pair for
PRIDE_0001012 in the PRIDE_0001012 class and its annotation block: include an
oboInOwl:hasExactSynonym for env_local_scale and add the matching
GSCMIXS:0000013 xref in the owl:Axiom alongside the existing IAO_0000115
annotation so the PRIDE and MIXS mappings stay aligned.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
| <!-- http://purl.obolibrary.org/obo/PRIDE_0001011 --> | ||
|
|
||
| <owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0001011"> | ||
| <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000017"/> | ||
| <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000458"/> | ||
| <obo:IAO_0000115>Report the major environmental system the sample or specimen came from (MIXS:0000012).</obo:IAO_0000115> | ||
| <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace> | ||
| <oboInOwl:id>PRIDE:0001011</oboInOwl:id> | ||
| <rdfs:label>broad-scale environmental context</rdfs:label> | ||
| </owl:Class> | ||
| <owl:Axiom> | ||
| <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0001011"/> | ||
| <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/> | ||
| <owl:annotatedTarget>Report the major environmental system the sample or specimen came from (MIXS:0000012).</owl:annotatedTarget> | ||
| <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref> | ||
| </owl:Axiom> | ||
|
|
There was a problem hiding this comment.
🗄️ Data Integrity & Integration | 🟡 Minor | ⚡ Quick win
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
set -euo pipefail
# Inspect the target region and similar MIXS-derived terms in pride_cv.owl
git ls-files | rg '(^|/)(pride_cv\.owl|pride_cv\.obo)$'
echo '--- target region ---'
sed -n '19970,20040p' pride_cv.owl
echo '--- similar terms with exact synonym / xref patterns ---'
rg -n -C 3 'env_medium|geo_loc_name|samp_collect_method|soil_type|soil_horizon|env_broad_scale|env_local_scale' pride_cv.owl
echo '--- exact synonym axiom patterns ---'
rg -n -C 2 'hasExactSynonym|hasDbXref>GSCMIXS:' pride_cv.owlRepository: PRIDE-Archive/pride-ontology
Length of output: 50384
🏁 Script executed:
#!/bin/bash
set -euo pipefail
echo '--- pride_cv.obo entries for PRIDE:0001011 / PRIDE:0001012 ---'
rg -n -C 6 '^(id: PRIDE:0001011|id: PRIDE:0001012|name: broad-scale environmental context|name: local environmental context|synonym:|xref:|def:)' pride_cv.obo
echo '--- exact terms env_broad_scale / env_local_scale in pride_cv.obo ---'
rg -n -C 8 'env_broad_scale|env_local_scale|MIXS:0000012|MIXS:0000013|GSCMIXS:0000012|GSCMIXS:0000013' pride_cv.obo
echo '--- nearby source region around PRIDE:0001011 and PRIDE:0001012 ---'
python3 - <<'PY'
from pathlib import Path
text = Path('pride_cv.obo').read_text(errors='replace').splitlines()
targets = ['PRIDE:0001011', 'PRIDE:0001012']
for i,line in enumerate(text):
if any(t in line for t in targets):
start=max(0,i-5); end=min(len(text),i+25)
print(f'\n@@ around line {i+1} @@')
for j in range(start,end):
print(f'{j+1}:{text[j]}')
PYRepository: PRIDE-Archive/pride-ontology
Length of output: 50385
🏁 Script executed:
#!/bin/bash
set -euo pipefail
echo '--- exact OBO blocks for PRIDE:0001011 and PRIDE:0001012 ---'
awk '
BEGIN{show=0; n=0}
/^\[Term\]/{show=0}
/^id: PRIDE:0001011$/ || /^id: PRIDE:0001012$/{show=1; n=0}
show{print; n++}
show && n>20{show=0}
' pride_cv.obo
echo '--- exact synonym / xref occurrences near those ids ---'
rg -n -C 4 'PRIDE:0001011|PRIDE:0001012|env_broad_scale|env_local_scale|GSCMIXS:0000012|GSCMIXS:0000013|MIXS:0000012|MIXS:0000013' pride_cv.obo
echo '--- whether any exact synonym axioms exist for these terms in OWL ---'
rg -n -C 2 'PRIDE_0001011|PRIDE_0001012|hasExactSynonym|GSCMIXS:0000012|GSCMIXS:0000013' pride_cv.owl | sed -n '1,120p'Repository: PRIDE-Archive/pride-ontology
Length of output: 9375
Add the MIXS field-name synonyms for PRIDE:0001011 and PRIDE:0001012.
Both exports omit the standard hasExactSynonym/GSCMIXS pair for env_broad_scale and env_local_scale, unlike the neighboring MIXS-derived terms. Add those annotations to keep field-to-term mapping consistent.
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@pride_cv.owl` around lines 19994 - 20010, Add the missing MIXS field-name
synonym annotations for the PRIDE_0001011 and PRIDE_0001012 class entries so
they match the neighboring MIXS-derived terms. Update each owl:Class block to
include the standard hasExactSynonym and GSCMIXS pair for env_broad_scale and
env_local_scale, keeping the annotations consistent with the existing ontology
pattern and locating the changes by the PRIDE_0001011 and PRIDE_0001012 symbols.
| <!-- http://purl.obolibrary.org/obo/PRIDE_0001012 --> | ||
|
|
||
| <owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0001012"> | ||
| <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000017"/> | ||
| <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000458"/> | ||
| <obo:IAO_0000115>Report the entity or entities which are in the sample or specimen s local vicinity and which you believe have significant causal influences on your sample or specimen (MIXS:0000013).</obo:IAO_0000115> | ||
| <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace> | ||
| <oboInOwl:id>PRIDE:0001012</oboInOwl:id> | ||
| <rdfs:label>local environmental context</rdfs:label> | ||
| </owl:Class> | ||
| <owl:Axiom> | ||
| <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0001012"/> | ||
| <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/> | ||
| <owl:annotatedTarget>Report the entity or entities which are in the sample or specimen s local vicinity and which you believe have significant causal influences on your sample or specimen (MIXS:0000013).</owl:annotatedTarget> | ||
| <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref> | ||
| </owl:Axiom> | ||
| </rdf:RDF> |
There was a problem hiding this comment.
🗄️ Data Integrity & Integration | 🟡 Minor | ⚡ Quick win
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
set -euo pipefail
# Inspect the relevant region and the sibling term mentioned in the comment.
file="pride_cv.owl"
echo "== Nearby lines for PRIDE_0001011 and PRIDE_0001012 =="
sed -n '19970,20060p' "$file" | cat -n
echo
echo "== Search for PRIDE_0001011/0001012 axioms and exact synonyms =="
rg -n -C 3 'PRIDE_0001011|PRIDE_0001012|hasExactSynonym|GSCMIXS:0000013|MIXS:0000013' "$file"Repository: PRIDE-Archive/pride-ontology
Length of output: 50384
🏁 Script executed:
#!/bin/bash
set -euo pipefail
file="pride_cv.owl"
echo "== MIXS-related annotations =="
rg -n -C 2 'GSCMIXS:000001[23]|env_(broad|local)_scale|MIXS:000001[23]|hasExactSynonym' "$file" | sed -n '1,220p'
echo
echo "== PRIDE_0001011/0001012 blocks only =="
sed -n '20000,20040p' "$file" | cat -nRepository: PRIDE-Archive/pride-ontology
Length of output: 16242
🌐 Web query:
MIXS:0000013 env_local_scale GSCMIXS:0000013
💡 Result:
MIXS:0000013, commonly referred to by its alias env_local_scale, is a standardized term within the Minimum Information about any (x) Sequence (MIxS) reporting framework, which is developed by the Genomics Standards Consortium (GSC) [1][2][3]. The env_local_scale field is used to document the local environmental context of a sample or specimen [1][4]. Specifically, it requires reporters to identify entities in the immediate vicinity of the sample that are believed to have a significant causal influence on its characteristics or composition [5][6]. Key characteristics of this term include: - Purpose: To describe the local environment with a finer spatial grain than the broader environment (env_broad_scale) [5][6]. - Expected Values: It is recommended to use terms from the Environment Ontology (EnvO) [5][2]. For host-associated or plant-associated samples, terms from interoperable OBO Library ontologies (such as UBERON for anatomical sites or the Plant Ontology) are also accepted [2][6]. - Format: The value should generally follow a pattern of a term label and its associated ID, for example, "litter layer [ENVO:01000338]" [2][7]. - Requirement: In the MIxS schema, this is typically a required field for various environmental and biological packages [7][8][9]. The GSC provides guidelines for using EnvO in conjunction with MIxS to ensure consistent and interoperable metadata reporting [5][6].
Citations:
- 1: https://genomicsstandardsconsortium.github.io/mixs/0000013/
- 2: https://cmungall.github.io/mixs-source/env_local_scale/
- 3: https://genomicsstandardsconsortium.github.io/gensc.github.io/pages/standards/all-terms.html
- 4: https://microbiomedata.github.io/nmdc-schema/env_local_scale/
- 5: https://www.ebi.ac.uk/ols4/ontologies/gscmixs/properties/https%253A%252F%252Fw3id.org%252Fmixs%252F0000013
- 6: https://microbiomedata.github.io/submission-schema/env_local_scale/
- 7: https://genomicsstandardsconsortium.github.io/mixs-6-2-for-merge/env_local_scale/
- 8: https://genomicsstandardsconsortium.github.io/mixs6.2_release_candidate/0000013/
- 9: https://microbiomedata.github.io/mixs-6-2-release-candidate/0000013/
🏁 Script executed:
#!/bin/bash
set -euo pipefail
file="pride_cv.owl"
echo "== Any GSCMIXS annotations in the file =="
rg -n 'GSCMIXS:' "$file" || true
echo
echo "== Any exact synonyms on the MIXS-related block =="
sed -n '20008,20032p' "$file" | rg -n 'hasExactSynonym|hasDbXref|MIXS:0000012|MIXS:0000013|env_broad_scale|env_local_scale'
echo
echo "== Nearby MIXS-related class blocks with annotations, if any =="
rg -n -C 3 'MIXS:0000012|MIXS:0000013|env_broad_scale|env_local_scale|hasExactSynonym|hasDbXref' "$file" | sed -n '1,120p'Repository: PRIDE-Archive/pride-ontology
Length of output: 7719
Add the MIXS synonym/xref pair for PRIDE:0001012. PRIDE:0001012 maps to env_local_scale (MIXS:0000013), so add the oboInOwl:hasExactSynonym annotation and matching GSCMIXS:0000013 xref axiom here to keep the MIXS terms aligned.
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@pride_cv.owl` around lines 20013 - 20029, Add the missing MIXS synonym/xref
pair for PRIDE_0001012 in the PRIDE_0001012 class and its annotation block:
include an oboInOwl:hasExactSynonym for env_local_scale and add the matching
GSCMIXS:0000013 xref in the owl:Axiom alongside the existing IAO_0000115
annotation so the PRIDE and MIXS mappings stay aligned.
2 participants
This automated PR updates the OWL file corresponding to the OBO file
Summary by CodeRabbit